Perl 脚本无法访问 Tabix 文件夹

Question

我是运行来自 EMBL 的 Perl 脚本（可在此处 https://github.com/EMBL-EBI-GCA/reseqtrack/blob/master/scripts/variation_data/calculate_allele_frq_from_vcf.pl 找到）在 Ubuntu 16.10 下，我已按要求安装了 Vcftools 和 Tabix，并且都经过测试相应地工作。我使用以下命令执行脚本：

perl /home/[user]/calculate_allele_frq_from_vcf.pl \
-vcf /home/[user]/share/1000genomesPhase3VCFFiles/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz \
-sample_panel /home/[user]/share/1000genomesPhase3VCFFiles/integrated_call_samples_v3.20130502.ALL.panel \
-out_dir /home/[user]/Desktop/AlleleFrequency \
-tabix  /home/[user]/tabix-0.2.6 \
-vcftools_dir /home/[user]/vcftools_0.1.13 \
-region 1:1-10000 \
-pop CEU,FIN \

这个returns下面的错误

Smartmatch is experimental at /home/[user]/calculate_allele_frq_from_vcf.pl line 133.
Smartmatch is experimental at /home/[user]/calculate_allele_frq_from_vcf.pl line 144.
sh: 1: /home/[user]/tabix-0.2.6: Permission denied
Broken VCF header, no column names?
 at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 172.
    Vcf::throw(Vcf4_2=HASH(0x55761601d320), "Broken VCF header, no column names?") called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 866
    VcfReader::_read_column_names(Vcf4_2=HASH(0x55761601d320)) called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 601
    VcfReader::parse_header(Vcf4_2=HASH(0x55761601d320)) called at /home/[user]/vcftools_0.1.13/perl/vcf-subset line 121
    main::vcf_subset(HASH(0x557615b24558)) called at /home/[user]/vcftools_0.1.13/perl/vcf-subset line 12
Broken VCF header, no column names?
 at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 172.
    Vcf::throw(Vcf4_2=HASH(0x55fa53436f60), "Broken VCF header, no column names?") called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 866
    VcfReader::_read_column_names(Vcf4_2=HASH(0x55fa53436f60)) called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 601
    VcfReader::parse_header(Vcf4_2=HASH(0x55fa53436f60)) called at /home/[user]/vcftools_0.1.13/perl/fill-an-ac line 45
    main::fill_an_ac(undef) called at /home/[user]/vcftools_0.1.13/perl/fill-an-ac line 9
sh: 1: /home/[user]/tabix-0.2.6: Permission denied
Broken VCF header, no column names?
 at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 172.
    Vcf::throw(Vcf4_2=HASH(0x5607d059a190), "Broken VCF header, no column names?") called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 866
    VcfReader::_read_column_names(Vcf4_2=HASH(0x5607d059a190)) called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 601
    VcfReader::parse_header(Vcf4_2=HASH(0x5607d059a190)) called at /home/[user]/vcftools_0.1.13/perl/vcf-subset line 121
    main::vcf_subset(HASH(0x5607d00a1558)) called at /home/[user]/vcftools_0.1.13/perl/vcf-subset line 12
Broken VCF header, no column names?
 at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 172.
    Vcf::throw(Vcf4_2=HASH(0x556b8e952110), "Broken VCF header, no column names?") called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 866
    VcfReader::_read_column_names(Vcf4_2=HASH(0x556b8e952110)) called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 601
    VcfReader::parse_header(Vcf4_2=HASH(0x556b8e952110)) called at /home/[user]/vcftools_0.1.13/perl/fill-an-ac line 45
    main::fill_an_ac(undef) called at /home/[user]/vcftools_0.1.13/perl/fill-an-ac line 9
/home/[user]/Desktop/AlleleFrequency/calculated_fra.process3085.1.1-10000.CEU_FIN

由于某种原因，该脚本似乎没有访问 Tabix 的权限。我已经为执行脚本的用户（我）授予文件夹完整 read/write 权限。有什么想法吗？

Answer 1

您将 -tabix 设置为 /home/[user]/tabix-0.2.6，但代码似乎需要可执行文件的路径，而不是顶级目录。将 /bin/tabix 添加到路径中应该可以解决问题。

Perl 脚本无法访问 Tabix 文件夹

Perl script cannot access Tabix folder

perl

bioinformatics

vcftools

vcf-variant-call-format